Mercurial > repos > ecology > xarray_metadata_info

annotate xarray_select.py @ 5:00de53d18b99 draft default tip

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planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
author ecology
date Sun, 31 Jul 2022 21:22:03 +0000
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5
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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diff changeset
1 # xarray tool for:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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2 # - getting metadata information
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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3 # - select data and save results in csv file for further post-processing
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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4
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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5 import argparse
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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6 import os
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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7 import warnings
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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8
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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9 import geopandas as gdp
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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10
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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11 import pandas as pd
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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12
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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13 from shapely.geometry import Point
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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14 from shapely.ops import nearest_points
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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15
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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16 import xarray as xr
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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17
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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18
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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19 class XarraySelect ():
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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20 def __init__(self, infile, select="", outfile="", outputdir="",
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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21 latname="", latvalN="", latvalS="", lonname="",
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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22 lonvalE="", lonvalW="", filter_list="", coords="",
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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23 time="", verbose=False, no_missing=False,
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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24 tolerance=None):
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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25 self.infile = infile
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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26 self.select = select
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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27 self.outfile = outfile
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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28 self.outputdir = outputdir
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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29 self.latname = latname
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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30 if tolerance != "" and tolerance is not None:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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31 self.tolerance = float(tolerance)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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32 else:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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33 self.tolerance = -1
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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34 if latvalN != "" and latvalN is not None:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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35 self.latvalN = float(latvalN)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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36 else:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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37 self.latvalN = ""
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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38 if latvalS != "" and latvalS is not None:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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39 self.latvalS = float(latvalS)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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40 else:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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41 self.latvalS = ""
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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42 self.lonname = lonname
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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43 if lonvalE != "" and lonvalE is not None:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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44 self.lonvalE = float(lonvalE)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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45 else:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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46 self.lonvalE = ""
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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47 if lonvalW != "" and lonvalW is not None:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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48 self.lonvalW = float(lonvalW)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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49 else:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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50 self.lonvalW = ""
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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51 self.filter = filter_list
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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52 self.time = time
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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53 self.coords = coords
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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54 self.verbose = verbose
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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55 self.no_missing = no_missing
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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56 # initialization
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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57 self.dset = None
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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58 self.gset = None
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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59 if self.verbose:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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60 print("infile: ", self.infile)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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61 print("outfile: ", self.outfile)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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62 print("select: ", self.select)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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63 print("outfile: ", self.outfile)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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64 print("outputdir: ", self.outputdir)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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65 print("latname: ", self.latname)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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66 print("latvalN: ", self.latvalN)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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67 print("latvalS: ", self.latvalS)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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68 print("lonname: ", self.lonname)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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69 print("lonvalE: ", self.lonvalE)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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70 print("lonvalW: ", self.lonvalW)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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71 print("filter: ", self.filter)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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72 print("time: ", self.time)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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73 print("coords: ", self.coords)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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74
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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75 def rowfilter(self, single_filter):
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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76 split_filter = single_filter.split('#')
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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77 filter_varname = split_filter[0]
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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78 op = split_filter[1]
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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79 ll = float(split_filter[2])
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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80 if (op == 'bi'):
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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81 rl = float(split_filter[3])
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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82 if filter_varname == self.select:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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83 # filter on values of the selected variable
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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84 if op == 'bi':
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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diff changeset
85 self.dset = self.dset.where(
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
86 (self.dset <= rl) & (self.dset >= ll)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
87 )
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
88 elif op == 'le':
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
89 self.dset = self.dset.where(self.dset <= ll)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
90 elif op == 'ge':
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ecology
parents:
diff changeset
91 self.dset = self.dset.where(self.dset >= ll)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
92 elif op == 'e':
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
93 self.dset = self.dset.where(self.dset == ll)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
94 else: # filter on other dimensions of the selected variable
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ecology
parents:
diff changeset
95 if op == 'bi':
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
96 self.dset = self.dset.sel({filter_varname: slice(ll, rl)})
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
97 elif op == 'le':
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
98 self.dset = self.dset.sel({filter_varname: slice(None, ll)})
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
99 elif op == 'ge':
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
100 self.dset = self.dset.sel({filter_varname: slice(ll, None)})
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
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101 elif op == 'e':
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ecology
parents:
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102 self.dset = self.dset.sel({filter_varname: ll},
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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103 method='nearest')
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ecology
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104
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ecology
parents:
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105 def selection(self):
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ecology
parents:
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106 if self.dset is None:
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ecology
parents:
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107 self.ds = xr.open_dataset(self.infile)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
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108 self.dset = self.ds[self.select] # select variable
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ecology
parents:
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109 if self.time:
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ecology
parents:
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110 self.datetime_selection()
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ecology
parents:
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111 if self.filter:
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ecology
parents:
diff changeset
112 self.filter_selection()
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ecology
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113
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ecology
parents:
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114 self.area_selection()
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ecology
parents:
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115 if self.gset.count() > 1:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
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116 # convert to dataframe if several rows and cols
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ecology
parents:
diff changeset
117 self.gset = self.gset.to_dataframe().dropna(how='all'). \
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
118 reset_index()
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ecology
parents:
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119 self.gset.to_csv(self.outfile, header=True, sep='\t')
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ecology
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120 else:
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ecology
parents:
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121 data = {
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
122 self.latname: [self.gset[self.latname].values],
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
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123 self.lonname: [self.gset[self.lonname].values],
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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124 self.select: [self.gset.values]
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
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125 }
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ecology
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126
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ecology
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127 df = pd.DataFrame(data, columns=[self.latname, self.lonname,
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ecology
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128 self.select])
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ecology
parents:
diff changeset
129 df.to_csv(self.outfile, header=True, sep='\t')
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130
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ecology
parents:
diff changeset
131 def datetime_selection(self):
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ecology
parents:
diff changeset
132 split_filter = self.time.split('#')
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
133 time_varname = split_filter[0]
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
134 op = split_filter[1]
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
135 ll = split_filter[2]
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
136 if (op == 'sl'):
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
137 rl = split_filter[3]
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
138 self.dset = self.dset.sel({time_varname: slice(ll, rl)})
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
139 elif (op == 'to'):
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
140 self.dset = self.dset.sel({time_varname: slice(None, ll)})
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
141 elif (op == 'from'):
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
142 self.dset = self.dset.sel({time_varname: slice(ll, None)})
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
143 elif (op == 'is'):
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
144 self.dset = self.dset.sel({time_varname: ll}, method='nearest')
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
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145
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ecology
parents:
diff changeset
146 def filter_selection(self):
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ecology
parents:
diff changeset
147 for single_filter in self.filter:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
148 self.rowfilter(single_filter)
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ecology
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149
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ecology
parents:
diff changeset
150 def area_selection(self):
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ecology
parents:
diff changeset
151
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
152 if self.latvalS != "" and self.lonvalW != "":
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
153 # Select geographical area
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ecology
parents:
diff changeset
154 self.gset = self.dset.sel({self.latname:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
155 slice(self.latvalS, self.latvalN),
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
156 self.lonname:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
157 slice(self.lonvalW, self.lonvalE)})
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
158 elif self.latvalN != "" and self.lonvalE != "":
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
159 # select nearest location
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ecology
parents:
diff changeset
160 if self.no_missing:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
161 self.nearest_latvalN = self.latvalN
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ecology
parents:
diff changeset
162 self.nearest_lonvalE = self.lonvalE
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
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163 else:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
164 # find nearest location without NaN values
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
165 self.nearest_location()
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
166 if self.tolerance > 0:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
167 self.gset = self.dset.sel({self.latname: self.nearest_latvalN,
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
168 self.lonname: self.nearest_lonvalE},
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
169 method='nearest',
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
170 tolerance=self.tolerance)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
171 else:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
172 self.gset = self.dset.sel({self.latname: self.nearest_latvalN,
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
173 self.lonname: self.nearest_lonvalE},
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
174 method='nearest')
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
175 else:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
176 self.gset = self.dset
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
177
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
178 def nearest_location(self):
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
179 # Build a geopandas dataframe with all first elements in each dimension
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
180 # so we assume null values correspond to a mask that is the same for
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
181 # all dimensions in the dataset.
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
182 dsel_frame = self.dset
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
183 for dim in self.dset.dims:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
184 if dim != self.latname and dim != self.lonname:
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
185 dsel_frame = dsel_frame.isel({dim: 0})
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
186 # transform to pandas dataframe
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
187 dff = dsel_frame.to_dataframe().dropna().reset_index()
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
188 # transform to geopandas to collocate
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
189 gdf = gdp.GeoDataFrame(dff,
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
190 geometry=gdp.points_from_xy(dff[self.lonname],
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
191 dff[self.latname]))
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
192 # Find nearest location where values are not null
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
193 point = Point(self.lonvalE, self.latvalN)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
194 multipoint = gdf.geometry.unary_union
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
195 queried_geom, nearest_geom = nearest_points(point, multipoint)
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
196 self.nearest_latvalN = nearest_geom.y
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
197 self.nearest_lonvalE = nearest_geom.x
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
198
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
199 def selection_from_coords(self):
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
200 fcoords = pd.read_csv(self.coords, sep='\t')
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
201 for row in fcoords.itertuples():
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
202 self.latvalN = row[0]
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
203 self.lonvalE = row[1]
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
204 self.outfile = (os.path.join(self.outputdir,
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
205 self.select + '_' +
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
206 str(row.Index) + '.tabular'))
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
207 self.selection()
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
208
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
209
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
210 if __name__ == '__main__':
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
211 warnings.filterwarnings("ignore")
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
212 parser = argparse.ArgumentParser()
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
213
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
214 parser.add_argument(
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
215 'infile',
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
216 help='netCDF input filename'
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
217 )
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
218 parser.add_argument(
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
219 '--select',
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
220 help='Variable name to select'
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
221 )
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
222 parser.add_argument(
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
223 '--latname',
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
224 help='Latitude name'
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
225 )
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
226 parser.add_argument(
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
227 '--latvalN',
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
228 help='North latitude value'
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
229 )
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
230 parser.add_argument(
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
231 '--latvalS',
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
232 help='South latitude value'
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
233 )
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
234 parser.add_argument(
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
235 '--lonname',
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
236 help='Longitude name'
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
237 )
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
238 parser.add_argument(
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
239 '--lonvalE',
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
240 help='East longitude value'
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
241 )
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
242 parser.add_argument(
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
243 '--lonvalW',
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
244 help='West longitude value'
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
245 )
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
246 parser.add_argument(
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
247 '--tolerance',
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
248 help='Maximum distance between original and selected value for '
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
249 ' inexact matches e.g. abs(index[indexer] - target) <= tolerance'
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
250 )
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
251 parser.add_argument(
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
252 '--coords',
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
253 help='Input file containing Latitude and Longitude'
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
254 'for geographical selection'
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
diff changeset
255 )
00de53d18b99 planemo upload for repository https://github.com/galaxyecology/tools-ecology/tree/master/tools/data_manipulation/xarray/ commit fd8ad4d97db7b1fd3876ff63e14280474e06fdf7
ecology
parents:
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256 parser.add_argument(
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257 '--filter',
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258 nargs="*",
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259 help='Filter list variable#operator#value_s#value_e'
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260 )
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261 parser.add_argument(
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262 '--time',
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263 help='select timeseries variable#operator#value_s[#value_e]'
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264 )
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265 parser.add_argument(
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266 '--outfile',
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267 help='csv outfile for storing results of the selection'
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268 '(valid only when --select)'
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269 )
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270 parser.add_argument(
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271 '--outputdir',
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272 help='folder name for storing results with multiple selections'
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273 '(valid only when --select)'
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274 )
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275 parser.add_argument(
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276 "-v", "--verbose",
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277 help="switch on verbose mode",
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278 action="store_true"
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279 )
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280 parser.add_argument(
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281 "--no_missing",
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282 help="""Do not take into account possible null/missing values
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283 (only valid for single location)""",
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284 action="store_true"
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285 )
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286 args = parser.parse_args()
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287
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288 p = XarraySelect(args.infile, args.select, args.outfile, args.outputdir,
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289 args.latname, args.latvalN, args.latvalS, args.lonname,
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290 args.lonvalE, args.lonvalW, args.filter,
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291 args.coords, args.time, args.verbose,
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292 args.no_missing, args.tolerance)
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293 if args.select:
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294 p.selection()